Ligand profile

883

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_00051 — DNA gyrase subunit B

Via homolog PDB 4p8o UniProt Q6GKU0 Formula C₁₉H₁₆FN₇O
Mol. weight 377.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
883
PDB
4p8o
UniProt (similar protein)
Q6GKU0
Target protein
KP13_00051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 377.38 Da
LogP (Crippen) 3.36
H-bond donors 3
H-bond acceptors 5
TPSA 108.48 Ų
Rotatable bonds 4
Aromatic rings 4 / 4
Heavy atoms 28
Fraction sp³ C 0.11
Formula C₁₉H₁₆FN₇O

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 108.5
  • −1 ≤ LogP ≤ 5 3.36
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 377.4
  • LogP ≤ 5 3.36
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 108.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)Nc1[nH]c2c(cc(cc2n1)c3cc(cnc3)F)c4ncccn4
InChI 
InChI=1S/C19H16FN7O/c1-2-22-19(28)27-18-25-15-8-11(12-6-13(20)10-21-9-12)7-14(16(15)26-18)17-23-4-3-5-24-17/h3-10H,2H2,1H3,(H3,22,25,26,27,28)
InChIKey 
FKCGKEHVIVGGDU-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF02518

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00051.

PDB 87

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)